From: Spyros C. <s.c...@gm...> - 2012-08-31 15:22:00
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Dear PyMOL community, I have a python script that reads a directory of ~500 homology models generated from a pipeline (I used a PDB file as a template to generate the models). It extracts residues that have charge-bearing atoms on them. When using GREP/EGREP to query a specific coordinate (e.g. 29.010) against the dataset and to determine which and in how many homology models it is present, the output looks like so: ./tem1_mod445.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 ./tem1_mod446.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 ./tem1_mod461.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 ./tem1_mod179.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049 ./tem1_mod180.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049 and so forth..... The ./tem1_mod**** string refers to the specific homology model file that contains the atom. *QUESTION* Once I have collected all atoms that I possess z-coordinates values within a range (29 - 54), Is there a way to map these onto a template PDB structure (in my case 3NY8 - adrenergic receptor). In other words, having collected hundreds of atomic coordinates (all from charged residues and all with z-values between 29.000 - 54.000 angstroms) across several different homology models (my dataset contains ~500 models) is there a way to visualize (using the z-coordinate spatial value as the criterion) them on a single PDB file? The reason I would like to do this is to observe any patterns in the occurrence of charge throughout the transmembrane region of receptor proteins. Many thanks in advance. Regards, Spyros Charonis |
From: Thomas H. <sp...@us...> - 2012-09-03 07:39:09
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Hi Spyros, so you want to visualize how often each atom matches your GREP query? You could put that count number as b-factor and then do a spectrum coloring. Example: python # load one of the homology models cmd.load('tem1_mod445.pdb') # set b-factor to zero for all atoms cmd.alter('all', 'b=0') # increment b-factor for each GREP line for line in open('output.txt'): line = line.split(':', 1)[-1] name = line[12:16] resi = line[22:26] cmd.alter('resi %s and name %s' % (resi, name), 'b=b+1') # show spheres, colored from yellow to red according to count cmd.show_as('spheres') cmd.spectrum('b', 'yellow_red', quiet=0) python end Cheers, Thomas Spyros Charonis wrote, On 08/31/12 17:21: > Dear PyMOL community, > > I have a python script that reads a directory of ~500 homology models > generated from a pipeline (I used a PDB file as a template to generate > the models). > It extracts residues that have charge-bearing atoms on them. When using > GREP/EGREP to query a specific coordinate (e.g. 29.010) against the dataset > and to determine which and in how many homology models it is present, > the output looks like so: > > ./tem1_mod445.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 > > ./tem1_mod446.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 > > ./tem1_mod461.pdb:ATOM CE1 HIS A 130 -3.832 -1.260 29.010 > > > ./tem1_mod179.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049 > > ./tem1_mod180.pdb:ATOM NZ LYS A 151 -12.607 8.920 29.049 > > > and so forth..... > > The ./tem1_mod**** string refers to the specific homology model file > that contains the atom. > > QUESTION > Once I have collected all atoms that I possess z-coordinates values > within a range (29 - 54), Is there a way to map these onto a template PDB > structure (in my case 3NY8 - adrenergic receptor). In other words, > having collected hundreds of atomic coordinates (all from charged > residues and > all with z-values between 29.000 - 54.000 angstroms) across several > different homology models (my dataset contains ~500 models) > is there a way to visualize (using the z-coordinate spatial value as the > criterion) them on a single PDB file? > The reason I would like to do this is to observe any patterns in the > occurrence of charge throughout the transmembrane region of receptor > proteins. > > Many thanks in advance. > > Regards, > Spyros Charonis -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen |